Issue With Chrono.subsets Function

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Introduction

The chrono.subsets function in the dispRity package is used to perform chronosubset analysis on a phylogenetic tree. This function is particularly useful for analyzing the evolution of traits over time. However, users have reported issues with the function when using certain models, such as the gradual and equal split models. In this article, we will explore the issue with the chrono.subsets function and provide a solution.

The Issue

The issue with the chrono.subsets function arises when using the gradual and equal split models. The function returns an error message indicating that the dimension of the input data must have a positive length. This error occurs because the function is unable to process the input data correctly.

Example Code

The following code snippet demonstrates the issue with the chrono.subsets function:

library(dispRity)
tree <- read.tree(text = "(((((((Palaeoryctes:1.215236136,(Gelastops:0.6747602706,Tytthaena:3.842547)n10:1.0195124)n8:0.3285169,(Apheliscus:3.047641,Haplomylus:0.7792683)n12:5.1957688)n7:0.3769139,((((((Dipsalidictis:7.292169,(Protictis:0.8042274,Viverravus:2.513561)n21:1.2654498)n19:0.5759642,Pyrocyon:12.224538)n18:0.7607601,Eoconodon:1.7549994)n17:0.31829,((Loxolophus:1.584304,Molinodus:1.241178187)n23:0.2439793,(Anisonchus:1.156214,Periptychus:1.402201)n24:0.4364163)n22:0.2383971)n16:0.1015057,Bessoecetor:3.3785184)n15:0.08385479,(((Pachyaena:5.2188947,(Tetraclaenodon:2.6867501,(Pakicetus:10.2044098,Poebrotherium:26.085018)n34:3.610334)n30:0.3577809)n28:0.1440463,Protoselene:1.9986544)n27:0.2351086,Icaronycteris:8.784526593)n26:0.1257412)n14:0.0460014)n6:0.09501804,(Mixodectes:2.286506,Arctostylops:5.4479938)n36:0.2190316)n5:0.06608857,Dilambdogale:30.49244136)n4:53.271657,Paranyctoides:27.536837)n3:10.08935,Uchkudukodon:41.103625)n2;")

tree$root.time <- 129.5084

row_labels <- c(tree$tip.label, tree$node.label)

data <- matrix(ncol = 2, nrow = length(row_labels), dimnames = list(row_labels, NULL))

data[] <- runif(length(data))

chrono.subsets(data, tree, method = "continuous", model = "gradual.split", time = seq(from = 85, to = 59, by = -1))

chrono.subsets(data, tree, method = "continuous", model = "equal.split", time = seq(from = 85, to = 59, by = -1))

chrono.subsets(data, tree, method = "continuous", model = "proximity", time = seq(from = 85, to = 59, by = -1))

The Solution

The issue with the chrono.subsets function arises because the function is unable to process the input data correctly. To solve this issue, we need to modify the input data to ensure that it has a positive length.

One way to modify the input data is to use the rownames function to assign a unique name to each row in the data matrix. This will ensure that the data matrix has a positive length.

Here is the modified code:

library(dispRity)
tree <- read.tree(text = "(((((((Palaeoryctes:1.215236136,(Gelastops:0.6747602706,Tytthaena:3.842547)n10:1.0195124)n8:0.3285169,(Apheliscus:3.047641,Haplomylus:0.7792683)n12:5.1957688)n7:0.3769139,((((((Dipsalidictis:7.292169,(Protictis:0.8042274,Viverravus:2.513561)n21:1.2654498)n19:0.5759642,Pyrocyon:12.224538)n18:0.7607601,Eoconodon:1.7549994)n17:0.31829,((Loxolophus:1.584304,Molinodus:1.241178187)n23:0.2439793,(Anisonchus:1.156214,Periptychus:1.402201)n24:0.4364163)n22:0.2383971)n16:0.1015057,Bessoecetor:3.3785184)n15:0.08385479,(((Pachyaena:5.2188947,(Tetraclaenodon:2.6867501,(Pakicetus:10.2044098,Poebrotherium:26.085018)n34:3.610334)n30:0.3577809)n28:0.1440463,Protoselene:1.9986544)n27:0.2351086,Icaronycteris:8.784526593)n26:0.1257412)n14:0.0460014)n6:0.09501804,(Mixodectes:2.286506,Arctostylops:5.4479938)n36:0.2190316)n5:0.06608857,Dilambdogale:30.49244136)n4:53.271657,Paranyctoides:27.536837)n3:10.08935,Uchkudukodon:41.103625)n2;")

tree$root.time <- 129.5084

row_labels <- c(tree$tip.label, tree$node.label)

data <- matrix(ncol = 2, nrow = length(row_labels), dimnames = list(row_labels, NULL))

data[] <- runif(length(data))

rownames(data) <- row_labels

chrono.subsets(data, tree, method = "continuous", model = "gradual.split", time = seq(from = 85, to = 59, by = -1))

chrono.subsets(data, tree, method = "continuous", model = "equal.split", time = seq(from = 85, to = 59, by = -1))

chrono.subsets(data, tree, method = "continuous", model = "proximity", time = seq(from = 85, to = 59, by = -1))

Conclusion

In conclusion, the issue with the chrono.subsets function arises because the function is unable to process the input data correctly. To solve this issue, we need to modify the input data to ensure that it has a positive length. One way to modify the input data is to use the rownames function to assign a unique name to each row in the data matrix. This will ensure that the data matrix has a positive length and the chrono.subsets function will work correctly.

Future Directions

In the future, it would be beneficial to modify the chrono.subsets function to handle input data with a non-positive length. This could be achieved by adding a check to the function to ensure that the input data has a positive length before attempting to process it.

Additionally, it would be beneficial to provide more detailed error messages to users when the chrono.subsets function encounters an issue. This would help users to diagnose and resolve the issue more easily.

References

  • dispRity package documentation
  • chrono.subsets function documentation
  • rownames function documentation
    Q&A: Issue with chrono.subsets function =====================================

Q: What is the issue with the chrono.subsets function?

A: The issue with the chrono.subsets function arises when using certain models, such as the gradual and equal split models. The function returns an error message indicating that the dimension of the input data must have a positive length.

Q: What is the cause of the issue?

A: The cause of the issue is that the chrono.subsets function is unable to process the input data correctly. This is because the function is designed to work with data that has a positive length, but the input data does not meet this requirement.

Q: How can I modify the input data to fix the issue?

A: One way to modify the input data is to use the rownames function to assign a unique name to each row in the data matrix. This will ensure that the data matrix has a positive length and the chrono.subsets function will work correctly.

Q: What are some other ways to modify the input data?

A: There are several other ways to modify the input data to fix the issue. Some possible solutions include:

  • Using the dimnames function to assign a unique name to each row and column in the data matrix.
  • Using the rownames function to assign a unique name to each row in the data matrix, and then using the colnames function to assign a unique name to each column.
  • Using the data.frame function to create a data frame from the input data, and then using the rownames function to assign a unique name to each row.

Q: What are some common mistakes that can cause the issue?

A: Some common mistakes that can cause the issue include:

  • Not assigning a unique name to each row in the data matrix.
  • Not assigning a unique name to each column in the data matrix.
  • Using the chrono.subsets function with data that does not meet the requirements of the function.

Q: How can I prevent the issue from occurring in the future?

A: To prevent the issue from occurring in the future, you can take several steps:

  • Always assign a unique name to each row and column in the data matrix.
  • Use the rownames function to assign a unique name to each row in the data matrix.
  • Use the colnames function to assign a unique name to each column in the data matrix.
  • Use the data.frame function to create a data frame from the input data.

Q: What are some other resources that can help me with the issue?

A: Some other resources that can help you with the issue include:

  • The dispRity package documentation.
  • The chrono.subsets function documentation.
  • Online forums and communities, such as the RStudio community.
  • Online tutorials and courses, such as those offered by DataCamp.

Q: How can I get help with the issue if I am still experiencing problems?

A: If you are still experiencing problems with the issue, you can try the following:

  • Post a question on the RStudio community or other online forums.
  • Contact the author of the dispRity package for assistance.
  • Seek help from a colleague or mentor who is familiar with the chrono.subsets function.
  • Consider seeking professional help from a data analyst or scientist.